For decades, breeders have known that chilling requirement (CR) varies wildly among peach cultivars—from under 100 hours to over 1,500 hours—but the trait’s genetic complexity has made it notoriously difficult to select for. Most known CR-related genes, particularly the well-studied DAM (Dormancy-Associated MADS-box) genes, explain only part of the picture, and existing molecular markers often fail when tested across genetically diverse populations. Breeding programs, especially those in low-latitude regions, have lacked reliable tools to identify low-CR genotypes. Based on these challenges, the team set out to conduct a comprehensive genome-wide association study (GWAS) across a uniquely diverse peach collection to uncover novel CR loci and develop robust, broadly applicable markers for marker-assisted selection.
The study (DOI: 10.1093/hr/uhag069), published on March 5, 2026, in Horticulture Research, was led by researchers from the Institute of Pomology at the Jiangsu Academy of Agricultural Sciences and Nanjing Agricultural University. The team performed GWAS on 213 peach accessions with CR phenotypes collected over three years, identifying 52 significant single nucleotide polymorphisms (SNPs) associated with CR, including novel loci on chromosomes 1 and 2.
The researchers first confirmed that CR is highly heritable, with a broad-sense heritability of 0.86—meaning more than 86% of the variation in CR among accessions is due to genetic differences. Phenotypic data collected over multiple years showed strong inter-annual correlations (r = 0.87–0.93), establishing a reliable foundation for association mapping. The GWAS revealed major CR-associated SNP clusters on chromosome 1 (17.3–21.2 Mb and 43.7–47.3 Mb) and chromosome 2 (5.2–13.9 Mb). Notably, while the previously reported DAM gene cluster on chromosome 1 was confirmed, the team also discovered novel loci in regions not previously linked to CR—findings that would have been missed in less diverse germplasm panels. From these, they developed 20 Kompetitive Allele Specific PCR (KASP) markers and rigorously validated them across 287 accessions. Two markers—Chr01:43706671 and Chr01:46470090—stood out for their predictive power. Used together, they correctly identified 95.5% of extreme low-CR accessions (CR < 300 hours) while maintaining 93.5% specificity against mid-to-high CR types. The markers also pinpointed three candidate genes with differential expression patterns between low- and high-CR cultivars during dormancy: a receptor-like protein kinase (Prupe.1G570300), a serine/threonine protein kinase (Prupe.1G025200), and a BED-type zinc finger domain-containing protein (Prupe.1G534800).
“What excites us most is that these markers actually work in the field—not just in controlled experiments, but across a wide range of peach varieties from different origins,” the authors said. “The fact that we can now predict extreme low-CR genotypes with over 95% accuracy means breeders in warm-winter regions finally have a practical tool to select for climate-adapted peaches. And the three genes we identified—especially the BED-type zinc finger protein and the receptor-like kinase—open entirely new avenues for understanding how plants measure and respond to cold. This is just the beginning.”
The two validated KASP markers offer an immediate, cost-effective solution for peach breeding programs worldwide. Breeders can now screen seedlings at the DNA stage, eliminating the need for years of field trials to determine CR. For growers in subtropical regions like southern China, where the study’s germplasm collection was specifically enriched, these markers enable the rapid introgression of low-CR alleles into locally adapted varieties. The markers also serve as a powerful exclusion tool: their exceptionally high negative predictive value (96.3%) allows breeders to confidently discard varieties unlikely to perform well under insufficient winter chill. Beyond breeding, the candidate genes identified—particularly the receptor-like kinase and the BED-type zinc finger protein—provide new molecular handles for dissecting the complex regulatory network that governs bud dormancy, potentially informing genetic engineering or gene-editing strategies in the future.
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References
DOI
10.1093/hr/uhag069
Original Source URL
https://doi.org/10.1093/hr/uhag069
Funding information
This work was supported by the China Agriculture Research System (CARS-30), Species Conservation Project of the Ministry of Agriculture and Rural Affairs (19210895), National Crop Germplasm Resources Infrastructure in China (NHGRC2020-NH16), The Open Competition Project of Seed Industry Revitalization of Jiangsu Province (Grant no. JBGS(2021)016), Accurate Identification of Peach and Strawberry Germplasm Resources in southern China (19230697), Peach and Strawberry (Southern) Germplasm Safe Preservation (19240424), and Species Conservation Project of Crop Germplasm Resources (Peach and Strawberry) in Jiangsu Province (2023-SJ-011).
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.